Literature DB >> 15215389

ConSite: web-based prediction of regulatory elements using cross-species comparison.

Albin Sandelin1, Wyeth W Wasserman, Boris Lenhard.   

Abstract

ConSite is a user-friendly, web-based tool for finding cis-regulatory elements in genomic sequences. Predictions are based on the integration of binding site prediction generated with high-quality transcription factor models and cross-species comparison filtering (phylogenetic footprinting). By incorporating evolutionary constraints, selectivity is increased by an order of magnitude as compared to single-sequence analysis. ConSite offers several unique features, including an interactive expert system for retrieving orthologous regulatory sequences. Programming modules and biological databases that form the foundation of the ConSite service are freely available to the research community. ConSite is available at http:/www.phylofoot.org/consite.

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Year:  2004        PMID： 15215389      PMCID： PMC441510          DOI： 10.1093/nar/gkh372

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  17 in total

Review 1.  DNA binding sites: representation and discovery.

Authors:  G D Stormo
Journal:  Bioinformatics       Date:  2000-01       Impact factor: 6.937

Review 2.  In silico identification of metazoan transcriptional regulatory regions.

Authors:  Wyeth W Wasserman; William Krivan
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3.  JASPAR: an open-access database for eukaryotic transcription factor binding profiles.

Authors:  Albin Sandelin; Wynand Alkema; Pär Engström; Wyeth W Wasserman; Boris Lenhard
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

4.  Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome.

Authors:  F Tronche; F Ringeisen; M Blumenfeld; M Yaniv; M Pontoglio
Journal:  J Mol Biol       Date:  1997-02-21       Impact factor: 5.469

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Authors:  D A Tagle; B F Koop; M Goodman; J L Slightom; D L Hess; R T Jones
Journal:  J Mol Biol       Date:  1988-09-20       Impact factor: 5.469

6.  Human-mouse genome comparisons to locate regulatory sites.

Authors:  W W Wasserman; M Palumbo; W Thompson; J W Fickett; C E Lawrence
Journal:  Nat Genet       Date:  2000-10       Impact factor: 38.330

7.  Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes.

Authors:  S Aparicio; A Morrison; A Gould; J Gilthorpe; C Chaudhuri; P Rigby; R Krumlauf; S Brenner
Journal:  Proc Natl Acad Sci U S A       Date:  1995-02-28       Impact factor: 11.205

8.  Phylogenetic footprinting reveals a nuclear protein which binds to silencer sequences in the human gamma and epsilon globin genes.

Authors:  D L Gumucio; H Heilstedt-Williamson; T A Gray; S A Tarlé; D A Shelton; D A Tagle; J L Slightom; M Goodman; F S Collins
Journal:  Mol Cell Biol       Date:  1992-11       Impact factor: 4.272

9.  Quantitative discrimination of MEF2 sites.

Authors:  J W Fickett
Journal:  Mol Cell Biol       Date:  1996-01       Impact factor: 4.272

10.  Regulation of the human cardiac/slow-twitch troponin C gene by multiple, cooperative, cell-type-specific, and MyoD-responsive elements.

Authors:  T H Christensen; H Prentice; R Gahlmann; L Kedes
Journal:  Mol Cell Biol       Date:  1993-11       Impact factor: 4.272
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Authors:  Jennifer R Kulzer; Michael L Stitzel; Mario A Morken; Jeroen R Huyghe; Christian Fuchsberger; Johanna Kuusisto; Markku Laakso; Michael Boehnke; Francis S Collins; Karen L Mohlke
Journal:  Am J Hum Genet       Date:  2014-01-16       Impact factor: 11.025

6.  An Intronic Enhancer Element Regulates Angiotensin II Type 2 Receptor Expression during Satellite Cell Differentiation, and Its Activity Is Suppressed in Congestive Heart Failure.

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7.  VEGFA rSNPs, transcriptional factor binding sites and human disease.

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8.  Human dopamine beta-hydroxylase (DBH) regulatory polymorphism that influences enzymatic activity, autonomic function, and blood pressure.

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9.  Identification and characterization of odorant-binding protein 1 gene from the Asian malaria mosquito, Anopheles stephensi.

Authors:  M S Sengul; Z Tu
Journal:  Insect Mol Biol       Date:  2009-11-10       Impact factor: 3.585

10.  Lack of CCAAT enhancer binding protein beta (C/EBPbeta) in uterine epithelial cells impairs estrogen-induced DNA replication, induces DNA damage response pathways, and promotes apoptosis.

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Journal:  Mol Cell Biol       Date:  2010-01-19       Impact factor: 4.272
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